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Isis sees its collaborative revenue soar, but higher R&D expenses and the lack of a one-time benefit causes its losses to balloon in the fourth quarter.

Antisense drug developer Isis Pharmaceuticals(NASDAQ:IONS) released its fourth-quarter earnings results before the opening bell this morning, pointing to a sizable uptick in recognized revenue, but also seeing its losses widen significantly from the year-ago period.

For the quarter, Isis reported total revenue of $42.2 million compared to just $19.9 million in the year-ago quarter, a 113% improvement. Research and development revenue due to its numerous collaborative agreements, rose to $41.3 million compared to $17.9 million during this quarter last year. Isis also tacked on nearly $1 million in licensing and royalty revenue.

Net loss, however, widened from just $2.6 million, or $0.03 per share, in the fourth quarter last year, to $24.3 million, or $0.21 per share as reported this morning. There were two primary reasons for this wider loss. First, research and development expenses soared by 34% to $57.4 million as Isis' pipeline has expanded to include later-stage studies, and even more experimental therapies. Secondly, Isis recognized a gain of $18.4 million last year from an investment in Regulus Therapeutics that wasn't present this year.

Since Isis is currently unprofitable, its remaining cash and cash burn rate are important. Isis ended the quarter with $656.8 million in cash, cash equivalents, and short-term investments, which was up notably from the $374.4 million it reported at the end of fiscal 2012. Isis attributed this leap to the $225 million in cash received from its drug development partners in 2013, as well as the $236 million raised via a share offering.

Looking ahead, Isis is projecting a fiscal 2014 net operating loss in the low $50 million range, consistent with the $51.7 million it lost from operations in fiscal 2013, and anticipates ending the year with more than $575 million in cash, implying a cash burn rate of around $80 million.

From a clinical perspective, Isis plans to end 2014 with three drugs in phase 3 development and another 10 in phase 2 development. Isis' CFO, Elizabeth Hougen, also noted in the press release that Isis has earned more than $16 million via its partners year-to-date.

Sean Williams has no material interest in any companies mentioned in this article. You can follow him on CAPS under the screen name TMFUltraLong, track every pick he makes under the screen name TrackUltraLong, and check him out on Twitter, where he goes by the handle @TMFUltraLong.

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A Fool since 2010, and a graduate from UC San Diego with a B.A. in Economics, Sean specializes in the healthcare sector and investment planning. You'll often find him writing about Obamacare, marijuana, drug and device development, Social Security, taxes, retirement issues and general macroeconomic topics of interest. Follow @TMFUltraLong